The Judge found that it was mandatory for the council to encourage participation by the Christian community and employees' representatives in the process, and that the council did not give the "requisite encouragement".
"Council's failure to encourage and obtain the views of those parties means its decision was made with insufficient information on those views," he said.
"The Council did not meet its obligation to encourage participation by the First Union, or other employee representatives, who were clearly a vitally interested sector of the community."
He also agreed on claims that public communication before debating the issue had been inadequate, particularly in relation to a request by Gwynn for more time.
"If the extent of public communication of the proposal was otherwise adequate, which I do not accept, then the Council could be found separately to have breached its obligation to encourage involvement given its response to Dr Gwynn's protest," Justice Dobson said.
"In a context such as this, declining a request for more time is the antithesis of encouraging that affected sector of the community to participate."
He added however there was not a complete failure to conduct consultation, saying: "The errors are rather inadequacies in the way it was carried out. The rights of potential submitters were infringed so that the errors are indeed more than technical."
Asked if he was pleased with the outcome, Gwynn, who the Judge said is entitled to costs, said: "I'm certainly relieved, because there were obvious consequences if not successful."
"But it's fundamentally important, because the council doesn't understand its obligations," he said. "That could explain quite a few things, because it seems to be upsetting a lot of people."
He said it had been not so much one of the potential workers loss of another "break day" as about the quality of the consultation.
"I am concerned that anyone should be forced to go to the High Court to be listened to," he said.